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- PDB-1l0e: X-ray Crystal Structure of AmpC K67Q Mutant beta-Lactamase -

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Basic information

Entry
Database: PDB / ID: 1l0e
TitleX-ray Crystal Structure of AmpC K67Q Mutant beta-Lactamase
Componentsbeta-lactamase
KeywordsHYDROLASE / amide hydrolase / beta-lactamase / mutant enzyme
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBeadle, B.M. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural bases of stability-function tradeoffs in enzymes.
Authors: Beadle, B.M. / Shoichet, B.K.
History
DepositionFeb 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-lactamase
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2693
Polymers79,1742
Non-polymers951
Water9,206511
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6822
Polymers39,5871
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,5871
Polymers39,5871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.022, 76.077, 98.094
Angle α, β, γ (deg.)90.00, 115.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-lactamase / Cephalosporinase


Mass: 39586.871 Da / Num. of mol.: 2 / Mutation: K67Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: K12 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Details: used to seeding, Usher, K.C., (1998) Biochemistry, 37, 16082.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 Msodium potassium phosphate1reservoirpH8.7
210 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 23, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 62018 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.3
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 243730
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FSY

1fsy


Resolution: 1.9→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.192 2193 Random
Rwork0.159 --
all-62018 -
obs-54456 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.702 Å20 Å2-1.132 Å2
2---0.659 Å20 Å2
3---1.361 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.096 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5590 0 5 511 6106
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_mcbond_it1.1711.5
X-RAY DIFFRACTIONc_scbond_it1.9582
X-RAY DIFFRACTIONc_mcangle_it1.7862
X-RAY DIFFRACTIONc_scangle_it2.9622.5
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection
Rfree0.223 181
Rwork0.181 -
obs-4034
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4sucrose.par
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 3.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.73

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